Showing : kegg • reset
0
votes
13
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15k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
2.9 years ago Laia ▴ 10
3
votes
13
replies
4.7k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
3.5 years ago • updated 3.1 years ago nute11a ▴ 10
0
votes
13
replies
7.5k
views
gage pathways enrichment analysis
gage pathways kegg
updated 11.2 years ago by ★ 1.6k • written 11.3 years ago by ▴ 100
5
votes
13
replies
4.5k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
22 months ago fernanda.backsouza ▴ 30
7
votes
11
replies
3.6k
views
Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 8.0 years ago by 53k • written 8.0 years ago by ▴ 60
4
votes
11
replies
6.0k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 2.8 years ago by • 0 • written 3.0 years ago by ▴ 10
1
vote
9
replies
4.2k
views
Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
KEGG keggrest
updated 7.9 years ago by ▴ 10 • written 7.9 years ago by ▴ 20
2
votes
8
replies
3.4k
views
GOseq package: Which genes are included in the "numDEInCat"?
GOseq KEGG
9.1 years ago Xavier ▴ 10
1
vote
7
replies
5.0k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 3.0 years ago by ▴ 780 • written 3.0 years ago by ▴ 10
4
votes
6
replies
4.0k
views
A good alternative for RDavidWebService ??
functional annotation KEGG RDavidWebService
10.7 years ago alakatos ▴ 130
7
votes
6
replies
3.9k
views
Interpretation of mroast gene set analysis in R and appropriate use of the function barcode plot regarding a microarray dataset
limma mroast barcodeplot KEGG gene set testing
updated 10.2 years ago by 53k • written 10.2 years ago by ▴ 840
6
votes
6
replies
6.4k
views
Finding enriched pathways from a gene list.
microarray limma kegg ENTREZ enrichment analysis
updated 6.0 years ago by 53k • written 6.0 years ago by ▴ 50
0
votes
6
replies
7.6k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
4.6 years ago Bogdan ▴ 670
4
votes
6
replies
6.4k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 3.5 years ago by ★ 4.1k • written 3.7 years ago by ▴ 10
2
votes
6
replies
5.5k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 2.1 years ago by ★ 4.1k • written 3.0 years ago by ▴ 10
0
votes
5
replies
3.1k
views
enrichKEGG function error
cluster clusterProfiler KEGG
2.8 years ago ruba-mahmoud • 0
0
votes
5
replies
2.6k
views
Gene set enrichment analysis for GO categories and KEGG pathway
GO KEGG
10.2 years ago libya.tahani • 0
0
votes
5
replies
2.4k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 2.9 years ago by • 0
1
vote
5
replies
4.2k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 4.6 years ago by • 0 • written 7.6 years ago by ▴ 40
6
votes
5
replies
2.5k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 4.9 years ago by ★ 1.6k • written 4.9 years ago by • 0
0
votes
5
replies
3.8k
views
Gene Symbol with Pathview
pathview bioconductor kegg visualization
updated 10.4 years ago by ★ 1.6k • written 10.4 years ago by • 0
0
votes
5
replies
3.5k
views
How to use topGO and KEGG with de-novo species
topgo edger limma kegga kegg
updated 8.5 years ago by 53k • written 8.5 years ago by ▴ 10
1
vote
4
replies
1.1k
views
pathview - multiple states
pathview Pathways KEGG
14 months ago Philippine • 0
1
vote
4
replies
2.5k
views
Indirect path in KEGG, activation or inhibition?
bioconductor graphite kegg pathway analysis
updated 9.0 years ago by ▴ 100 • written 9.0 years ago by • 0
2
votes
4
replies
3.1k
views
Can't find gene list for KEGG genesets
kegg geneset genelist gage package
updated 8.5 years ago by 53k • written 8.5 years ago by ▴ 30
4
votes
4
replies
3.0k
views
How I interpret this plot from pathview
pathview kegg r pathway
6.3 years ago • updated 6.2 years ago AZ ▴ 20
2
votes
4
replies
2.8k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
written 22 months ago by • 0
0
votes
4
replies
3.5k
views
Drawing custom KEGG pathways
pathview KEGG
written 4.8 years ago by ▴ 10
1
vote
4
replies
2.5k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
2.7 years ago Jiyoung Lee • 0
1
vote
4
replies
1.4k
views
How to apply KEGG enrichment analysis to the overlap of multiple contrasts in MArrayLM fit?
limma kegg
updated 7.4 years ago by 53k • written 7.4 years ago by ▴ 10
5
votes
4
replies
2.5k
views
Function kegga not working for species other than the conventional ones - Pathways do not overlap with universe
kegga limma pathway analysis kegg
updated 6.8 years ago by 53k • written 6.8 years ago by ▴ 60
4
votes
4
replies
11k
views
Packages for GO and KEGG analysis on RNAseq data
GO gage goseq KEGG
updated 11.4 years ago by 53k • written 11.5 years ago by ▴ 120
0
votes
4
replies
4.2k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 16 months ago by • 0 • written 2.4 years ago by • 0
2
votes
3
replies
6.1k
views
Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 4.6 years ago by • 0 • written 10.2 years ago by ▴ 20
1
vote
3
replies
3.1k
views
Pathview pathview kegg.native=TRUE throws error in img
pathview kegg error bioconductor rnaseq
updated 8.3 years ago by ▴ 40 • written 9.0 years ago by ▴ 30
1
vote
3
replies
2.0k
views
Ortholog conversions of non-model organisms not present in Biomart, ensembl or KEGG
rnaseq_analysis KEGG nonmodel species
updated 7.4 years ago by 68k • written 7.4 years ago by • 0
1
vote
3
replies
3.4k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 2.0 years ago by • 0 • written 3.7 years ago by • 0
1
vote
3
replies
2.3k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
0
votes
3
replies
1.7k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
3.6 years ago abf ▴ 30
1
vote
3
replies
2.7k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 2.9 years ago by ★ 4.1k • written 2.9 years ago by ▴ 10
0
votes
3
replies
1.8k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 5.7 years ago by 68k • written 5.7 years ago by ▴ 670
0
votes
3
replies
2.1k
views
kegga error from edgeR
edger r bioconductor pathway analysis kegg
updated 8.0 years ago by 53k • written 8.0 years ago by ▴ 120
0
votes
3
replies
2.0k
views
CHiPpeakAnno GO and/or KEGG results presenting
chippeakanno go kegg graphics
9.9 years ago lokapal • 0
1
vote
3
replies
2.5k
views
Regarding the issue of background genes in enrichment analysis
KEGG goTools seqTools
written 7 months ago by ▴ 10
1
vote
3
replies
2.3k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
10.0 years ago serpalma.v ▴ 60
0
votes
3
replies
1.3k
views
pathview error
KEGGgraph KEGG
updated 21 months ago by ★ 4.1k • written 21 months ago by • 0
1
vote
2
replies
3.1k
views
Error in Pathview parsing: "Parsing ./ko00195.xml file failed, please check the file!"
pathview KEGG parsing
8.3 years ago ladypurrsia ▴ 10
1
vote
2
replies
2.5k
views
GeneAnswer for bacteria metagenomes
geneanswers metagenome kegg
updated 9.6 years ago by ★ 1.2k • written 11.3 years ago by ▴ 100
0
votes
2
replies
1.8k
views
how to build gene.pathway data.frame for non-model organism
limma kegg topgo dataframe edger
8.5 years ago mictadlo ▴ 10
0
votes
2
replies
4.6k
views
Accessing KEGG (errors w/ KEGGREST)
KEGG keggrest
updated 9.1 years ago by 53k • written 9.1 years ago by • 0
113 results • Page 1 of 3
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Answer: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
I'm not familiar with the packages you mention, but the whole reason why Bioconductor has versions is that code and annotation change. Code…
Comment: Question on processing compound protein groups in limpa by JKim • 0
Many thanks. I appreciate your advice.
Answer: Question on processing compound protein groups in limpa by Gordon Smyth 53k
Different people have different ways of dealing with compound protein groups. You could just leave them in the analysis, in which case limp…
Answer: Correct usage of limpa for protein input by Gordon Smyth 53k
limpa can work on protein-level quantifications, but they must be intensity-based and must be on the log scale. From what I read (<https://…
Comment: A problem occurs when running the monocle2 by a2a2hset32aa • 0
Troubleshooting monocle2 errors in R 4.5.1 often points to package incompatibilities, particularly with newer versions of igraph. For resea…
Votes
Answer: Question on processing compound protein groups in limpa
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
A: Interpretaion of dendrogram height in WGCNA?
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